In sub-Saharan Africa, the majority of the haplotypes fall within one of three groups (groups I–III in fig. 1) sharing the ancestral allelic state at the M89 locus. In contrast, the majority of non-African chromosomes carry the derived allele at this locus (groups VI–X in fig.1). The only notable exception in sub-Saharan Africa is represented by a set of chromosomes that harbors the M207 and M173 mutations (haplotype 117 in fig. 1) and is found in different linguistic groups of northern Cameroon, at an average frequency of 40%. These two mutations define all members of group IX (haplotypes 110–123 in the study by Underhill et al. [2001b]), ahaplogroup that shares the M9 mutation with haplogroups VII, VIII, and X (haplotypes 81–96, 97–109, and 124–131, respectively, in the study by Underhill et al.[2001b]). So far, all group IX chromosomes from Europe and the Middle East that we analyzed were found to carry either the M269 mutation (haplotype 117b and derivatives) or the SRY10831 and M17 mutations (haplotypes 119–122). Both of these groups of haplotypes are very common in western Eurasia but harbor opposite frequency clines (R.S., unpublished data; P.A.U., unpublisheddata). Haplotypes carrying the SRY10831 mutation are not restricted to western Eurasia but are also common in central, northern, and southern Asia (Hammer et al. 2001; Karafet et al. 2001). Exclusive to Asia is a third group IX lineage, characterized by the M73 mutation (haplotype 123). The fourth and last group IX lineage identified so far is represented by the Cameroonian haplotype 117, which lacks any known downstream mutations.How can the presence of Group IX chromosomes at considerable frequency in Cameroon be explained? A priori, we can envision three possibilities. First, group IX chromosomes in Cameroon are due to rather recent male gene flow from Europe or the Near East. Second,the entire M9 superclade (haplogroups VII–X) has an African origin. Third, group IX chromosomes in Cameroon represent a footprint of a male back migration from Asia to Africa. The first scenario seems to be very unlikely, because only derived haplotypes, carrying theM269 or M17/SRY10831 mutations, have been detected in western Eurasia. The second hypothesis, an African origin of the M9 superclade that includes haplotype 117, would imply a subsequent impressive extinction of derivative lineages in sub-Saharan Africa, since no other haplotypes carrying the M9 mutation (haplogroups VII–X) have been observed in this region (the only exception being represented by a few haplotype 109 chromosomesfound in the Fulbe from Cameroon). The last scenario, that of a back migration from Asia to Africa, currently appears to be by far the most plausible. This is because most of the M9 haplotypes (the majority of group VII and VIII lineages, as well as some group IX and X lineages reported by Underhill et al. [2000]) have been observed only in Asia. Moreover, this possibility appears to be further supported by the recent finding of the UTY2+/M173- intermediate haplotype (Karafet et al. 2001) in central and northeastern Asia (the UTY2marker in the study by Karafet et al. [2001] corresponds to M207 in the present study).On the basis of phylogeographic Y-haplotype analyses, Asia has been regarded as the source of several old migrations leading to the peopling of America, Oceania, and Europe (Karafet et al. 1999; Santos et al. 1999; Hammer et al. 2001; Underhill et al. 2001b; Wells et al. 2001; Lell et al. 2002). In particular, M173-bearing chromosomes in Europe are considered to delineate an ancient expansion from Asia during the Upper Paleolithic,~ 30,000 years ago (Semino et al. 2000; Underhill et al. 2001b; Wells et al. 2001). It is quite reasonable to hypothesize that an ancient Asian gene pool was the source of both the European (haplotype 117b) and Cameroonian (haplotype 117) M173 chromosomes. The fact that haplotype 117 is rare or absent in Asia (P.A.U., unpublished data) or the Middle East (present study), suggests that a large portion of its microsatellite diversity in Cameroon accumulated within the African continent after the proposed back-migration event, probably as a consequence of a population expansion. The coalescence age of the African haplotype 117, which we estimated as 4,100 years (95% CI 2,400–8,060 years), could thus represent a date for such an expansion and a lower limit for the time of entry into Africa. The occurrence of the latter event may not necessarily be recent. Although anthropological evidence indicates recent movements between western Asia and Africa by pastoralists Cavalli-Sforza et al. 1994), the phylogeography and diversity patterns of M173-associated lineages suggest an earlier demographic history. The absence in northern Cameroon of Y haplotypes affiliated with the recolonization of Europe following the Last Glacial Maximum, as well as the subsequent Neolithic transition (Semino et al.2000), is consistent with this interpretation. Interestingly, phylogenetic analysis of primate T-cell lymphotropic viruses type 1 indicate a putative Asian origin (Vandamme et al. 1998) followed by a simian- or human-mediated introduction to Africa~ 20,000 years ago (Van Dooren et al. 2001).An ancient human back migration from Asia to Africa had already been proposed by Altheide and Hammer (1997) and Hammer et al. (1998, 2001), on the basis of nested cladistic analysis of Y-chromosome data. They suggested that the presence of YAP+ chromosomes in Africa was due to such an event, but this has recently been questioned by Underhill et al. (2001b) and Underhill and Roseman (2001), primarily on the basis of the Asian-specific YAP+ subclade that neutralizes the previous phylogenetic inferences. Thus, the only evidenceof a migration from Asia to sub-Saharan Africa that is fully supported by Y-chromosome data relies, at least for the moment, on the finding of haplogroup IX chromosomes in Cameroon. Interestingly, a frequency of 13% has been previously reported in an Egyptian sample for a group of chromosomes defined as haplotype 1C (Scozzari et al. 1999) and closely related to the M173 chromosomes. Unfortunately, this sample was not available for the present study. Although we cannot define more precisely the haplotype of the Egyptian 1C Y chromosomes, it is worth noting that four of six of these chromosomes showed dinucleotide microsatellite haplotypes that matched or were onestep neighbors of the M173 chromosomes found in Cameroon. The genetic uniqueness of the northern Cameroon populations outlined here is based entirely on Y-chromosome evidence. It is desirable that additional markersare examined to provide a complement to the Y-chromosome data. In particular, an mtDNA analysis might help to evaluate possible sex-specific differences in migratory behavior."

Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages.AbstractAlthough human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25* are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25* Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25* and about half of the few European/west Asian R-P25* chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9200–5600?kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.http://www.nature.com/ejhg/journal/vaop/ncurrent/abs/ejhg2009231a.html